Qian Liu
| Snapshot Date: 2026-02-20 13:40 -0500 (Fri, 20 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-21 11:32 -0500 (Sat, 21 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4871 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1772/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for ReUseData in R Universe. | ||||||||||||||
|
To the developers/maintainers of the ReUseData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ReUseData |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2026-02-21 03:15:28 -0500 (Sat, 21 Feb 2026) |
| EndedAt: 2026-02-21 03:18:14 -0500 (Sat, 21 Feb 2026) |
| EllapsedTime: 166.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 5.871 0.364 6.237
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ReUseData)
ReUseData.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ReUseData)
>
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
202e0c55c354df_GRCh38.primary_assembly.genome.fa.1.bt2 added
202e0c2ee97c7c_GRCh38.primary_assembly.genome.fa.2.bt2 added
202e0c4d92ff48_GRCh38.primary_assembly.genome.fa.3.bt2 added
202e0c71ae6de7_GRCh38.primary_assembly.genome.fa.4.bt2 added
202e0c362980f0_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
202e0c2ff24fbc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
202e0c6447e110_outfile.txt added
202e0c312d066f_GRCh37_to_GRCh38.chain added
202e0c172b15fc_GRCh37_to_NCBI34.chain added
202e0cbec7a34_GRCh37_to_NCBI35.chain added
202e0c7ae69476_GRCh37_to_NCBI36.chain added
202e0c31a28803_GRCh38_to_GRCh37.chain added
202e0c384fc86f_GRCh38_to_NCBI34.chain added
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202e0c6057f6c2_GRCh38_to_NCBI36.chain added
202e0c79c14b30_NCBI34_to_GRCh37.chain added
202e0c4d10bd97_NCBI34_to_GRCh38.chain added
202e0c747f74f9_NCBI35_to_GRCh37.chain added
202e0c366123cb_NCBI35_to_GRCh38.chain added
202e0c2841d7d6_NCBI36_to_GRCh37.chain added
202e0c26ae4ffb_NCBI36_to_GRCh38.chain added
202e0c717f239a_GRCm38_to_NCBIM36.chain added
202e0c3ffa1f77_GRCm38_to_NCBIM37.chain added
202e0c4ed60d35_NCBIM36_to_GRCm38.chain added
202e0c797f0486_NCBIM37_to_GRCm38.chain added
202e0c628654df_1000G_omni2.5.b37.vcf.gz added
202e0c47e08118_1000G_omni2.5.b37.vcf.gz.tbi added
202e0c1efcd3f8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
202e0c2aebda51_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
202e0c38dbc53b_1000G_omni2.5.hg38.vcf.gz added
202e0c92a00c1_1000G_omni2.5.hg38.vcf.gz.tbi added
202e0caf2f30_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
202e0c67c541b7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
202e0c56bd0009_af-only-gnomad.raw.sites.vcf added
202e0c725d9d17_af-only-gnomad.raw.sites.vcf.idx added
202e0c1deec2a7_Mutect2-exome-panel.vcf.idx added
202e0c6af4fc6_Mutect2-WGS-panel-b37.vcf added
202e0c56a57e27_Mutect2-WGS-panel-b37.vcf.idx added
202e0c4f1bc917_small_exac_common_3.vcf added
202e0c1dda65c2_small_exac_common_3.vcf.idx added
202e0c6291f85c_1000g_pon.hg38.vcf.gz added
202e0c4a025d8d_1000g_pon.hg38.vcf.gz.tbi added
202e0c4f7cedc5_af-only-gnomad.hg38.vcf.gz added
202e0c1ae1c0cb_af-only-gnomad.hg38.vcf.gz.tbi added
202e0c391b6877_small_exac_common_3.hg38.vcf.gz added
202e0c2fd4e488_small_exac_common_3.hg38.vcf.gz.tbi added
202e0c14a30bfb_gencode.v41.annotation.gtf added
202e0c62c260e_gencode.v42.annotation.gtf added
202e0c24545981_gencode.vM30.annotation.gtf added
202e0c4b042fc6_gencode.vM31.annotation.gtf added
202e0c2e6dfde4_gencode.v41.transcripts.fa added
202e0c4b02a97d_gencode.v41.transcripts.fa.fai added
202e0c3c835361_gencode.v42.transcripts.fa added
202e0c6e681d5b_gencode.v42.transcripts.fa.fai added
202e0c19d8b6b2_gencode.vM30.pc_transcripts.fa added
202e0c360257e7_gencode.vM30.pc_transcripts.fa.fai added
202e0c50ee723b_gencode.vM31.pc_transcripts.fa added
202e0c61b937cb_gencode.vM31.pc_transcripts.fa.fai added
202e0c54ff2bdf_GRCh38.primary_assembly.genome.fa.1.ht2 added
202e0c7bda4c8c_GRCh38.primary_assembly.genome.fa.2.ht2 added
202e0c1a94fd06_GRCh38.primary_assembly.genome.fa.3.ht2 added
202e0c5e292ca0_GRCh38.primary_assembly.genome.fa.4.ht2 added
202e0c7c897bbc_GRCh38.primary_assembly.genome.fa.5.ht2 added
202e0c25a3ebd_GRCh38.primary_assembly.genome.fa.6.ht2 added
202e0c34e62caa_GRCh38.primary_assembly.genome.fa.7.ht2 added
202e0c6ee718d3_GRCh38.primary_assembly.genome.fa.8.ht2 added
202e0c20490165_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
202e0c3b957c70_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
202e0c458c96fb_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
202e0c6f64ca7c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
202e0c596fe232_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
202e0c281e8f57_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
202e0c39672809_GRCh38_full_analysis_set_plus_decoy_hla.fa added
202e0c28eccff7_GRCh38.primary_assembly.genome.fa.fai added
202e0c43005022_GRCh38.primary_assembly.genome.fa.amb added
202e0c72829080_GRCh38.primary_assembly.genome.fa.ann added
202e0c58c1b47f_GRCh38.primary_assembly.genome.fa.bwt added
202e0c57a35c1e_GRCh38.primary_assembly.genome.fa.pac added
202e0c78aeb68f_GRCh38.primary_assembly.genome.fa.sa added
202e0c7d160e01_GRCh38.primary_assembly.genome.fa added
202e0c22a78be4_hs37d5.fa.fai added
202e0c271cb473_hs37d5.fa.amb added
202e0c4818b77e_hs37d5.fa.ann added
202e0c5f2adf45_hs37d5.fa.bwt added
202e0c1584d1cf_hs37d5.fa.pac added
202e0c61f16e30_hs37d5.fa.sa added
202e0c152d372c_hs37d5.fa added
202e0c6673440a_complete_ref_lens.bin added
202e0c43aaa5fb_ctable.bin added
202e0c6a2c630b_ctg_offsets.bin added
202e0c624d9096_duplicate_clusters.tsv added
202e0c5e3fa301_info.json added
202e0c48558fac_mphf.bin added
202e0c5ed70c52_pos.bin added
202e0c6099e1bf_pre_indexing.log added
202e0c7d3bbc56_rank.bin added
202e0c4dbe2525_ref_indexing.log added
202e0ce2e324_refAccumLengths.bin added
202e0c38d138c6_reflengths.bin added
202e0c134abc20_refseq.bin added
202e0c7047ada0_seq.bin added
202e0c12411af8_versionInfo.json added
202e0c3b694b77_salmon_index added
202e0c29aed5a9_chrLength.txt added
202e0c3b2deaef_chrName.txt added
202e0c7e699b9a_chrNameLength.txt added
202e0c1c31662a_chrStart.txt added
202e0c13ef9f6f_exonGeTrInfo.tab added
202e0c560cf7b8_exonInfo.tab added
202e0c14e01cb9_geneInfo.tab added
202e0c1105ad70_Genome added
202e0c78b4839c_genomeParameters.txt added
202e0c3bfcd12c_Log.out added
202e0c591e64ee_SA added
202e0c57df62e2_SAindex added
202e0c5181a2fb_sjdbInfo.txt added
202e0c3b0fd31e_sjdbList.fromGTF.out.tab added
202e0c6d0c9a0e_sjdbList.out.tab added
202e0c37f4e705_transcriptInfo.tab added
202e0c7eba791a_GRCh38.GENCODE.v42_100 added
202e0c5738fd1a_knownGene_hg38.sql added
202e0c1a42779b_knownGene_hg38.txt added
202e0c5cfa1c1b_refGene_hg38.sql added
202e0c1f8e8cc6_refGene_hg38.txt added
202e0c791983ed_knownGene_mm39.sql added
202e0c3d93fdda_knownGene_mm39.txt added
202e0c1cca491c_refGene_mm39.sql added
202e0c46d7a913_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes
Data is downloaded:
/tmp/Rtmp3COPyB/test_gcpData/outfile.txt
}[1;30mINFO[0m Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added
Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
17.641 1.124 19.296
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.871 | 0.364 | 6.237 | |
| dataSearch | 1.108 | 0.018 | 1.126 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.673 | 0.121 | 3.748 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.126 | 0.001 | 0.127 | |
| recipeLoad | 1.269 | 0.063 | 1.332 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.532 | 0.011 | 0.542 | |
| recipeUpdate | 0 | 0 | 0 | |